Skip Navigation



Bioinformatics Advance Access published online on January 25, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti257
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/9/2097    most recent
bti257v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Li, W.
Right arrow Articles by Farman, M. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Li, W.
Right arrow Articles by Farman, M. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics © Oxford University Press 2005; all rights reserved.
Received November 11, 2004
Accepted December 29, 2004

Applications note

TruMatch - A BLAST post-processor that identifies and reports bona fide sequence matches

Weixi Li 1, Cathryn J. Rehmeyer 2, Chuck Staben 1, and Mark L. Farman 2*

1 Department of Biological Sciences, University of Kentucky, Lexington, KY 40546
2 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546

* To whom correspondence should be addressed.
Mark L. Farman, E-mail: farman{at}uky.edu


  Abstract

Summary: BLAST is a widely-used alignment tool for detecting matches between a query sequence and entries in nucleotide sequence databases. Matches (high-scoring pairs) are assigned a score based on alignment length and quality and, by default, are reported with the top-scoring matches listed first. For certain types of searches, however, this method of reporting is not optimal. This is particularly true when searching a genome sequence with a query that was derived from the same genome, or a closely related one. If the genome is complex and the assembly is far from complete, correct matches are often relegated to low positions in the results, where they may easily be overlooked. To rectify this problem, we developed TruMatch - a program that parses standard BLAST outputs and identifies high-scoring pairs that involve query segments with unique matches to the assembly. Candidates for bona fide matches between a query sequence and a genome assembly are listed at the top of the TruMatch output.

Availability: TruMatch is written in Perl and is freely available to non-commercial users via web download at the URL: http://genome.kbrin.uky.edu/fungi_tel/TruMatch/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
C. Rehmeyer, W. Li, M. Kusaba, Y.-S. Kim, D. Brown, C. Staben, R. Dean, and M. Farman
Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae
Nucleic Acids Res., October 18, 2006; 34(17): 4685 - 4701.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.